package dr.evomodel.treelikelihood;
public class NativeCovarionLikelihoodCore extends AbstractLikelihoodCore {
public NativeCovarionLikelihoodCore() {
super(8);
}
protected void calculateIntegratePartials(double[] inPartials,
double[] proportions, double[] outPartials) {
nativeIntegratePartials(inPartials, proportions, patternCount, matrixCount, outPartials);
}
protected void calculatePartialsPartialsPruning(double[] partials1,
double[] matrices1, double[] partials2, double[] matrices2,
double[] partials3) {
nativePartialsPartialsPruning(partials1, matrices1, partials2, matrices2, patternCount, matrixCount, partials3);
}
protected void calculateStatesPartialsPruning(int[] states1,
double[] matrices1, double[] partials2, double[] matrices2,
double[] partials3) {
nativeStatesPartialsPruning(states1, matrices1, partials2, matrices2, patternCount, matrixCount, partials3);
}
protected void calculateStatesStatesPruning(int[] states1,
double[] matrices1, int[] states2, double[] matrices2,
double[] partials3) {
nativeStatesStatesPruning(states1, matrices1, states2, matrices2, patternCount, matrixCount, partials3);
}
protected void calculatePartialsPartialsPruning(double[] partials1,
double[] matrices1, double[] partials2, double[] matrices2,
double[] partials3, int[] matrixMap) {
throw new RuntimeException("not implemented using matrixMap");
}
protected void calculateStatesStatesPruning(int[] states1,
double[] matrices1, int[] states2, double[] matrices2,
double[] partials3, int[] matrixMap) {
throw new RuntimeException("not implemented using matrixMap");
}
protected void calculateStatesPartialsPruning(int[] states1,
double[] matrices1, double[] partials2, double[] matrices2,
double[] partials3, int[] matrixMap) {
throw new RuntimeException("not implemented using matrixMap");
}
public void calculateLogLikelihoods(double[] partials,
double[] frequencies, double[] outLogLikelihoods) {
int v = 0;
for (int k = 0; k < patternCount; k++) {
double sum = frequencies[0] * partials[v];
v++;
sum += frequencies[1] * partials[v];
v++;
sum += frequencies[2] * partials[v];
v++;
sum += frequencies[3] * partials[v];
v++;
sum += frequencies[4] * partials[v];
v++;
sum += frequencies[5] * partials[v];
v++;
sum += frequencies[6] * partials[v];
v++;
sum += frequencies[7] * partials[v];
v++;
outLogLikelihoods[k] = Math.log(sum) + getLogScalingFactor(k);
}
}
public native void nativeIntegratePartials(double[] partials, double[] proportions,
int patternCount, int matrixCount,
double[] outPartials);
protected native void nativePartialsPartialsPruning(double[] partials1, double[] matrices1,
double[] partials2, double[] matrices2,
int patternCount, int matrixCount,
double[] partials3);
protected native void nativeStatesPartialsPruning(int[] states1, double[] matrices1,
double[] partials2, double[] matrices2,
int patternCount, int matrixCount,
double[] partials3);
protected native void nativeStatesStatesPruning(int[] states1, double[] matrices1,
int[] states2, double[] matrices2,
int patternCount, int matrixCount,
double[] partials3);
public static boolean isAvailable() {
return isNativeAvailable;
}
private static boolean isNativeAvailable = false;
static {
try {
System.loadLibrary("CovarionLikelihoodCore");
isNativeAvailable = true;
} catch (UnsatisfiedLinkError e) {
System.err.println("Using Java general likelihood core " + e.toString());
}
}
}